taxonomy download from NCBI based on geneID
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Jitendra ▴ 10
@nabiyogesh-11718
Last seen 4 months ago
United Kingdom

Is it possible to download taxonomy based on gene Id for a large dataset from NCBI using biomartr package?

vi arsM.ID.txt

AAAK03000116.1
AAAL02000001.1
AACD01000079.1
AACS02000002.1
AADV02000002.1
AADV02000014.1
AADV02000142.1
AADV02000157.1
AADV02000160.1
AADV02000163.1
AAEK01000011.1
AAEK01000037.1
AAEW02000007.1
AAEW02000015.1
AAEW02000015.1

taxonomy format should be like below:

I need taxonomy in this format:

AM774418.1 Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Halobacterium  Halobacterium salinarum R1
LOPV01000533.1 Archaea; Euryarchaeota; Halobacteria; Haloferacales; Haloferacaceae; Haloferax  Haloferax sp. SB29
CP003125.1      Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus; Geobacillus thermoleovorans group  Geobacillus 
BAWP01000033.1  Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Parageobacillus Parageobacillus thermoglucosidasius NBRC 
MEFJ01000016.1  Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales; Thiobacillaceae; Thiobacillus   Thiobacillus sp. SCN 
FXAE01000009.1  Bacteria; Firmicutes; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus      Paenibacillus barengoltzii J12
biomartr Bioconducter • 829 views
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